Bit patterned media (BPM) disk manufacturing includes fabricating master-templates. Fabricating master-templates includes nano-imprint lithography processes. Nano-imprint lithography includes self-assembly processes to create high density patterns. Self-assembly processes create regular patterns such as hexagonal close packed or square structures used for creating BPM data-patterns. Two or more pattern overlay processes are added to create BPM of servo-patterns. Overlay misalignments create inaccuracies in the master templates.